School of Applied Sciences, REVA University, Rukmini Knowledge Park, Bangalore, 560064, Karnataka, India.
Basesolve Informatics Private Limited, Ellisbridge, Ahmedabad, 380006, Gujarat, India.
Arch Microbiol. 2022 Jul 14;204(8):481. doi: 10.1007/s00203-022-03100-8.
Agricultural productivity of pomegranate can be enhanced by identifying the crop-associated microbial diversity in the rhizosphere region with respect to plant growth promoters and other beneficial organisms. Traditional culture methods have limitations in microbial screening as only 1-2% of these organisms can be cultured. In the present study, 16S rRNA amplicon-based metagenomics approach using MinION Oxford Nanopore platform was employed to explore the microbial diversity in the rhizosphere of pomegranate Bhagwa variety, across variable soil depths from 0 to 5 cms (R2), 5-10 cms (R4) and 10-15 cms (R6), using bulk soil as the control. Across all the three layers, significant variations in pH, nitrogen content and total fungal count were observed. 16S rRNA analysis showed the abundance of planctomycetes, Pirellula staleyi, followed by bacteroidetes, Flavisolibacter LC59 and Niastella koreensis across the various soil depths in the rhizospheric soil samples. Pathway prediction analysis indicated arginine and proline metabolism (gamma-glutamyl putrescine oxidase) and hydrogen sulfide biosynthesis as the most abundant pathway hits. Comparative abundance analysis across layers showed the R6 layer with the maximum microbial diversity in terms of highest dimension of variation (79.2%) followed by R4 and R2 layers (p < 0.01). Our analysis shows the significant influence of root zone in shaping microbial diversity. This study has reported the presence of Planctomycetes, Pirellula staleyi for the first time in the pomegranate field.
通过鉴定与植物生长促进剂和其他有益生物相关的根际区作物相关微生物多样性，可以提高石榴的农业生产力。传统的培养方法在微生物筛选方面存在局限性，因为只有 1-2%的这些生物可以被培养。在本研究中，使用 MinION Oxford Nanopore 平台的 16S rRNA 扩增子宏基因组学方法，探索了 Bhagwa 品种石榴根际的微生物多样性，土壤深度从 0 到 5 厘米（R2）、5-10 厘米（R4）和 10-15 厘米（R6）不等，以散装土壤作为对照。在所有三个土层中，观察到 pH 值、氮含量和总真菌计数都有显著变化。16S rRNA 分析显示，在根际土壤样本中，与各种土壤深度相关的，是浮霉菌门的 Planctomycetes、Pirellula staleyi，其次是拟杆菌门的 Bacteroidetes、Flavisolibacter LC59 和 Niastella koreensis。途径预测分析表明，精氨酸和脯氨酸代谢（γ-谷氨酰腐胺氧化酶）和硫化氢生物合成是最丰富的途径。跨层比较丰度分析表明，R6 层以最高的维度变化（79.2%）显示出最大的微生物多样性，其次是 R4 和 R2 层（p<0.01）。我们的分析表明，根区对微生物多样性的形成有显著影响。本研究首次报道了根际区石榴中存在 Planctomycetes、Pirellula staleyi。
